a .pk3 isa form of compression.
I suggest downloading one of the following programs:
Winzip( works on .pk3 but is limited)
Winrar( opens the most files, and .pk3)
Or pakscape( .pk3 specific)
Then open a .pk3 of an existing map, and see how they organized their .pk3, when your ready to pack up the map, highlight all of the folders( that have the appropriate files in them) then right click, and winrar/winzip should have an option to pack it into a .zip.
Then change the extension to .pk3 and voila.